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Darwin John was hired by FBI director Robert Mueller and will replace Bob Dies, who served for two years as both chief information officer and assistant director for information resources at the FBI.
John, who has worked for the church since 1990, helped create the IT systems it uses to communicate with its 11 million members.
According to the FBI, John helped create the church's Family Search Web site, which has averaged seven to eight million hits a day since 1999. The site contains a database of some 900 million names for searching.
Mueller said that John brings demonstrated capabilities that can help the agency modernise its IT systems to fight terrorism.
John will be responsible for developing IT strategies to support the FBI's work and will report directly to Mueller.